A short throw would solve ur problem. I make custom shift knobs for guys here (mostly pool balls, perfect fit for big hands, but I can convert almost anything... including a dildo... yeah I did that once...). Biggest issue I get is the boot doesn't meet up to the knob. Some guys don't care. Some get a short throw or you can do this.

1. Take the knob and boot off.
2. Get a thin bolt 12mm x1.25 I think.
3. thread the bolt on to where the bottom of the knob is roughly. Put the boot on. The added bolt will hold the boot up to the knob. Put the knob back on.
4. Run through the gears making sure the boot has enough room to allow full engagement of the gears.

Other than that your screwed. They make smaller boots. But I've never seen a bigger one.